Duty First
by LMXB
Summary: When John becomes the target of revenge he must choose between his duty and protecting Jennifer, then live with the consequences.
1. Chapter 1

**Disclaimer**: I do not own SGA or any of the characters.

**A/N:** This is a short angsty story set shortly after the events of Missing.

_When John becomes the target of revenge he must choose between his duty and protecting Jennifer, then live with the consequences._

* * *

"Thanks for coming." Sam said as John entered his office.

"Seeing you're the boss I kinda assumed I didn't have much choice, but you're welcome." He smiled taking a seat. "What's up?"

"There is a mission scheduled to P2X-389." Sam explained.

"Giving aid to sick villagers?" John asked trying to remember the planet.

"That's the one. I'm thinking of sending Dr Keller, but wanted your opinion. Do you think she's ready for off-world travel after New Athos and the Bola Kai?"

"I'm not a shrink." John pointed out.

"I know that, I just wanted your gut instinct." Sam explained. "P2X-389 is fairly safe and she'll be escorted…"

"But you're concerned there are unresolved issues?" John guessed.

"You probably know more about what happened on New Athos than I do." Sam said, assuming Teyla had confided more details with John than she had put in the mission report. "We both know she was put in a situation she wasn't trained for."

"But she came through it." John pointed out. "Teyla said Keller showed potential."

"I know, I just have a niggling doubt if sending her out again is going to tip her. I don't want to loose our CMO."

"We can't have a CMO who doesn't go off-world." John pointed out.

"So you're happy for me to clear her for active duty?"

"Not my call." John replied. "But if you were to clear her I suggest my team accompanies her. If I spot any signs of PTSD I'll scrub the mission."

"That's what I was hoping you'd say." Sam smiled.

"In that case you can explain to McKay why he's not going to play in the lab tomorrow." John suggested.

"He's on your team, it'd be better coming from you." Sam countered. "Besides I need to tell Keller."

-00-

"Try not to look so nervous." John said as Jennifer, laden with bags entered the gateroom. "Rodney is really not that bad to be on a mission with."

"Ha ha." The physicist shot back.

"You all set?" John asked Jennifer.

"I think so."

"You'll be fine." Teyla assured Jennifer as she stood by her side.

"How about you?" Jennifer asked.

"I am fine." Teyla smiled confidently.

"Yes yes we're all fine. Can we go now? I want to get back by five." Rodney complained.

"Do I want to know why?" John asked.

"It's the finals tonight?"

"Tonight? You sure? I thought that was tomorrow."

"I'm so going to win." McKay said smugly.

Noticing Jennifer's confused look Teyla explained.

"They race toy cars."

"They're not toys." John protested.

"Sorry to interrupt, but are you ready?" Sam asked keen to get the team off.

"Yes ma'am." John said.

"Good. Let me know if there are any problems." She instructed John who gave a knowing look as Chuck dialled the gate.

-00-

"Is this going to take much longer?" Rodney complained as he sat outside the makeshift clinic.

"You could ask the doc again and delay her even further." John pointed out.

"How long does it take to deal with sick people….ooooh that's interesting." McKay said getting distracted by his computer.

"What's interesting?" John asked.

"I'm detecting an intermittent energy spike."

"A good spike?"

"Won't know until we look."

"Where is it coming from?"

"Half a mile out of the village." McKay explained.

John looked at his watch and then at his other bored teammates.

"Fine, Ronon, Teyla go with Rodney. I'll stay here and look after Keller. I want you back here in an hour."

As Rodney picked up his gear John looked at Teyla and Ronon and warned. "Make sure he doesn't stray too far."

"Of course." Teyla agreed.

When the trio had departed John strolled over to Jennifer's clinic to check on her progress. As he walked he remained oblivious to a group sitting in a bar watching his every move.

"How's it going doc?" John asked entering the building.

"Almost done. I hope."

"No rush, the others have gone off to look at an energy spike. They won't be back for an hour."

"Okay." Jennifer said as a stocky man entered the clinic. "Take a seat over there and I'll be right with you." Jennifer instructed the man.

John was going to leave, but his gut told him something was wrong, so instead he asked.

"You mind if I help out in here? It's kinda dull out there."

"Of course not. As long as you don't eat all my lollipops." Jennifer smiled as another man entered the clinic. As John turned to look at the new entrant the earlier one pulled a weapon and shot the Colonel. Before Jennifer could react she was also taken out with a single shot.

* * *

**A/N: **Thanks for reading and reviewing. Next chapter will be up in the next couple of days.


	2. Chapter 2

"Keller?" John questioned as he moved across the darkened cell to where the doctor still lay unconscious. When he reached her he gently shook her and was relieved when she started to stir.

"Colonel?" She asked groggily.

"Yeah, don't move to fast." He warned as he helped her slowly sit up. "Whatever they hit us with is still having an affect."

"Where are we?"

"No idea. I only came to a few minutes ago and have so far seen no one." John explained as he walked over to the cell door and tried to open it. When it didn't move he commented. "That would have been too easy." Turning back to Jennifer he asked. "You remember what happened?"

"Not really. You were shot, well stunned I guess."

"Got that part." John said sarcastically. He was about to comment further when he heard footsteps approaching. Backing away from the door and back to Jennifer he warned. "Someone's coming." Moments later someone shone a light through the bars momentarily blinding the pair of them.

"Good, you're awake. I was beginning to grow impatient." A man said as John heard keys enter a lock moments before the door swung open.

Struggling to see he tried to identify how many assailants there were and calculate an escape plan.

"Whatever you are thinking Colonel, I suggest you stop. My men are armed and well trained. There is no escape. If you cooperate neither of you will be harmed."

"Go to hell." John replied.

"You have no idea how much I was hoping you'd say that." The man smiled before turning to his men. "Bring them to the interrogation room."

Turning to Jennifer, John said. "It'll be okay." Before two burly men grabbed hold off him and dragged him away. Behind him he saw Jennifer suffer similar treatment.

As he was dragged down dark and dingy corridors he tried to remember the journey and identify anything that looked like an escape route. Finally he was pulled into a small dark room with a chair in the corner and a single light. As he was roughly tied to the chair he was relieved that he was the one who would be bearing the brunt of the rough treatment. That relief was ended when the man, who appeared to be the leader, explained.

"I want five things from you. Firstly, the address of Atlantis, secondly your GDO code, thirdly the address of your so called Alpha site, fourthly you master command codes for activating the Self destruct on Atlantis and finally to make you suffer."

As John heard the list, his first thought was concern that his captor knew so much, making the Colonel question who the man was. Before he came up with any answers the captor went on.

"To put things into context after we captured you we gated to several planets before coming here. You're people have no idea where you are and will not be mounting a rescue. You will be here until you die."

"Not exactly selling yourself here." John pointed out, glancing at Jennifer who was being held in the corner looking scared.

His captor sneered at him before asking. "So will you tell me what I want to know?"

"I'm going to go with no." John replied.

The captor gave John a sickening smile and then nodded at the guards who were holding Keller. One released his grasp on the doctor moments before unleashing a series of blows into her midrift.

"Hey." John shouted trying to free himself for the chair as the attack on Jennifer continued.

"I've thought long and hard about how to get what I want and the order in which to do things." The captor smiled as John looked on in dismay. "You see I want to destroy you and to do that I need to destroy Atlantis with your help. I could torture you and although it would be amusing, you're probably too much of a professional to give me anything. So instead I will make you watch as we torture your doctor. The woman you are responsible for protecting, in the knowledge you can stop it any moment by giving me what I want."

John continued to struggle against his restraints as Jennifer was bombarded with sickly blows. The onslaught continued until Jennifer passed out.

"You two will keep coming back here. Each time your doctor will receive similar treatment until you give me what I want." Their captor said before turning to the guards. "Take them back to their cell."

-00-

As Jennifer started to wake she moved causing a pain so sharp in her side she couldn't help but whimper. As memories of her beating started to flood back into her mind she felt two hands on her, causing her to tense until she heard John say.

"Doc? It's okay, it's just me."

"Colonel?" She asked trying to focus on the man before her. As she locked eyes with his all she could see was guilt.

"Try not to move." John instructed. "I don't know how much damage they did."

"I'm okay." Jennifer said weakly, trying to sound braver than she felt. "Will you help me sit up?"

"Sure that's wise?" John questioned, clearly concerned for her.

"I'm sure." Jennifer said, in too much pain to give any more of an answer.

Slowly and gently John helped Jennifer sit up against the cell wall. Once upright the young doctor closed her eyes trying to overcome the pain. Once she felt more in control she opened her eyes and saw John look on with concern.

"Doc, no matter what he said the others will find us." John said firmly.

"I know." Jennifer replied, trying to half smile. "I also know you won't give up the information."

"I'm sorry." John replied, his voice dripping with guilt.

"Don't be. I would hate Atlantis to be put in danger because of me." Jennifer said shutting her eyes as pain shot through her ribs.

"Are they broken?" John asked.

"Don't think so. Just bruised." Jennifer replied, although the Colonel wasn't sure if she was being truthful. Opening her eyes, revealing raw fear she asked. "When will they be back?"

"I don't know. Try not to think about it."

"I know. I should think about everything worth living for." Noticing John's surprise at her answer she explained. "Teyla's a good teacher."

"So what got you through the Bola Kai?"

"My dad. I'm all he has."

"Is that who you visited when you went back to Earth?" John questioned.

"Yeah."

"How'd he take you coming back roughed up?"

"He was confused and concerned. He wasn't sure how I could get injured when I'm in a lab all day. At first he thought I must be in a violent relationship. But apparently me falling down a flight of stairs was more believable than having a boyfriend, violent or not. The part of this job I hate the most is lying to him."

"Good luck explaining your injuries this time." John said. When he noticed Jennifer's sad look he said. "You are getting out of this."

"I know." Jennifer said, although her voice convinced neither of them that she was telling the truth. "How about you?" Jennifer asked. "Any family?"

"Not really."

"Significant other?"

"I'm not good at the whole sustaining a relationship thing." John said, before asking, turning the focus back onto Jennifer. "From your comment either I'm guessing you don't have a guy waiting for you?"

"No. No good at the whole starting a relationship thing." Jennifer explained just as they heard footsteps approach the cell.

Seeing Jennifer tense John said. "Think of your dad."

* * *

**A/N: **Thanks for reading and reviewing. Next chapter will be up in the next couple of days.


	3. Chapter 3

"Why are you doing this?" John asked as he was strapped into the chair in the interrogation room for the fifth time.

"Because you destroyed me and my family."

"Look, I really don't know who you are and if I am responsible for something I'm sorry. But Keller is innocent." John protested unable to watch more pain being inflicted on Jennifer.

"So was I and my family. But we were all banished. All of us became outcasts to our people. My daughter died because of the exile." The captor spat.

"Exile from where? Who are you?" John asked. For what seemed like a long time his captor said nothing, instead he turned and watched his men attack Jennifer. Eventually though he turned to John and said.

"Baccus Kolya."

"Relation of Acastus Kolya?" John asked, wondering if he would ever be free of the Kolya name.

"Brother. Sharing a name was enough to get us banished by Cowan."

"Cowan is dead." John said.

"Radim will not have us back, out of fear that it'll upset his precious treaty with your people. You condemned my family. The only way I can return to my people is if yours no longer exist. By destroying Atlantis I will not only destroy you, but I will be able to return to my people and lead them back to the glory they deserve."

"I am not responsible for your exile." John argued as Jennifer fell to the ground unconscious. "Even if I was, your exile dates back to before Keller was part of our team. She is innocent. You want revenge fine, but don't take it out on her. Let her go."

"She'll be my plaything and your weakness until she dies." Baccus said. "Unless you hand over what I want, but we both know you are too duty bound to do that. Either way I win." With that he turned from John ordering his men to return his captives to their cell.

-00-

Jennifer lay on the floor in the cell in too much pain to move. She thought back to her brief time with the Bola Kai and how scared she had felt. She remembered how she came through that ordeal not because of her own strength but because of Teyla's.

Behind her she heard John pace the length of the cell, presumably trying to find a weakness that had eluded him for the previous few days. As much as she wanted him to find an escape she lost faith of it happening.

She didn't know how much longer she could hold on. She wasn't even sure how long she had held on. She had lost count of the number of brutal beatings she had sustained and without natural light the only indication of time passing was John's lengthening stubble.

She wanted to be strong but she knew she was losing the battle. As much as John was a pillar of strength he was also a source of her weakness. Every time they talked she could see the guilt in his eyes. Guilt she knew he shouldn't be burdened with.

She could sense her hope was fading, but she couldn't let Sheppard see, his guilt was already overpowering. Feeling more scared than she had ever done and devoid of hope she clutched her ribs and silently cried, hoping to hide her fear from the Colonel, until she fell asleep.

-00-

Frustrated at his lack of power John glanced at Jennifer to ascertain if she was awake yet. He was concerned with how little she managed to remain conscious now, but he also thought it was for the best. As he resumed pacing he heard an almost whimper coming from Jennifer. Assuming it was another nightmare he picked up the stale bread and water that had been left for them and moved over to Jennifer. Gently placing a hand on Jennifer's shoulder he tried to coax her out of her nightmare.

When her panic stricken eyes opened he soothed. "It's okay. It's just me." He then waited for Jennifer to calm. "Try to drink this." John said as he held a cup to Jennifer's lips. Having watched her take a painful few sips he put the cup down and asked. "Anything I can do to help?"

"Can you help me sit?" Jennifer asked, finding the pressure on her lungs too much.

Nodding John maneuvered her as carefully as possible cursing himself every time he heard her hiss in pain. When she was finally upright and positioned against the wall he asked.

"Better?"

"Yes. Thanks." Jennifer said groggily as her eyes started to shut.

"Don't mention it." John replied as he sat next to her. Convinced she had fallen back to sleep Sheppard was surprised when he heard her say.

"Colonel?"

"Yeah."

"You think they're coming for us?"

"Don't doubt it for a second." Ignoring his own doubts he went on. "McKay and Carter will have come up with some clever way of tracking us. They'll come. Just try to hold on until they do." He paused and glanced down at her before going on. "Until they come think about what you'll do when you're back. Personally I'm thinking about a nice turkey sandwich and about how annoyed Rodney is going to be that he had to miss the race to find us. In fact he'll probably never let us forget it. When we finally get round to having the race and I beat him he'll accuse us of deliberately getting kidnapped to throw him off his game." His next planned sentence never came as he heard footsteps approaching again. Feeling Jennifer tremble next to him he squeezed her hand and said. "Hang on. They'll come."

* * *

**A/N: **Thanks for reading and reviewing. Next chapter will be up in the next couple of days.


	4. Chapter 4

John knew that Jennifer had nearly been broken. For the first few days he had seen her pain and fear, but subsequently he had seen the lost look in her eyes. He had heard her whimper in her sleep and tremble whenever the cell door opened. But what pained him the most was when she cried. She cried so quietly John was convinced it was so he didn't hear. The thought that Jennifer was trying to shield him from how scared she was magnified his guilt. He hated himself for not saving her and stopping her pain, but he wouldn't risk Atlantis. Even if he did he wasn't sure that Baccus Kolya would stop Jennifer's suffering. But either way, he would not risk Atlantis. He knew there were only three options available: escape; rescue; death. He also knew that the time may come when he became responsible for Jennifer's life in the same way he had been responsible for Colonel Sumner's. An action that still haunted him.

He had tried his best to keep Jennifer going, but each time she shared something of herself it made it that much harder to watch as she was attacked, whilst he was powerless to protect her.

He paced the cell once more desperate to find something that would help their escape. Hoping that their captors would accidently drop something useful as they entered the cell. He didn't need much, he had already frayed his bonds and in time he would break through them completely, but Jennifer did not have time.

As he paced, despite the darkness, something caught his eye. Moving to the door he saw the item sit by the cell entrance. Bending down he saw another shimmer as light reflected off a metallic object. As he picked it up it's edge caught his skin and drew blood. Despite a niggle in the back of his mind that his find had been too lucky he smiled and felt a glimmer of hope.

He stood and walked back to Jennifer and offered her some water. As he helped her drink it he said. "I have a plan."

-00-

As Jennifer hit the deck once more the pain radiated through her ribs. She wanted to shut her eyes, for everything to end, but she remembered John's words and knew she had to act. Mustering what strength she had left she cried.

"I'll tell you."

"Doc no." John shouted from his chair.

Ignoring the Colonel's outburst Baccus approached Jennifer and kneeled in front of her. Gripping her chin in his hand he forced her to look at him as he asked. "Tell me what?"

"The GDO code."

"You'll betray your comrades?" Baccus questioned.

"Just please stop." Jennifer whimpered, trying to keep the attention off John in the hope he could cut through his bonds.

"You people make me sick." Baccus said. "What is the code?" When Jennifer remained silent he hit her and demanded. "The code doctor or things will take a turn for the worse." Before Jennifer had the chance to reply Baccus heard a huge crash from behind. Turning he saw the two guards by Sheppard on the ground moments before John fired one of their weapons straight at Baccus.

Seeing Baccus crumble John took out the other two guards before walking over to Baccus and ensuring he was dead. When he saw their captor's chest move he fired several more rounds until he was convinced it was over. Finally convinced he crouched down in front of Jennifer.

"You did great doc. Can you walk?" He asked, knowing they had a better chance of escape if he had both his hands free. Shakily Jennifer nodded and allowed John to help her to her feet and guide her out of the room. John looked down at her and knew she was being driven solely by adrenaline, but with other options unavailable he could do nothing but be a guiding hand as they went through the darkened tunnels. They had only been going two minutes when he saw Jennifer wobble and almost fall.

"Not much further." He lied trying to offer her hope. Silently Jennifer kept walking behind John.

When John finally saw the far end of a tunnel brighten he started to let optimism take over. "Nearly there." He told Jennifer who once again remained silent. He brought a sudden halt to their progression though when he heard talking from what he assumed was an opening to the outside world. Hating to leave Jennifer, but knowing she would be a hindrance he helped Jennifer lean against a wall and whispered.

"Stay here. I'll be right back." He wasn't sure if Jennifer took in what he said but knew he had to face the next challenge alone. Glancing back at Jennifer he edged towards the light and the voices. The more he edged forward the more he was convinced he was approaching the exit as light spread through the tunnel and the air seemed to get less damp. When he finally reached the end of the tunnel he carefully peered out, pausing for a few seconds for his eyes to adjust. As he looked he saw the targets and was relieved there were only two of them. Raising the gun he had taken off one of his guards he quickly dispatched the men before stepping outside the tunnel. To his relief he didn't see anyone else. What he did see was a well-worn path, which he hoped led to the Stargate.

Turning he jogged back down the tunnel to Jennifer, who was no longer standing, but was sat leaning against the wall.

"I've cleared a path." He told her crouching down in front of the doctor. "You ready?"

"Not sure I can." She said her voice hitching. "Go without me." Despite her words John could see the fear and panic in her eyes. Taking her hand he said.

"Not a chance. We both go home or neither of us goes home. Now let's go."

With those words he helped her to her feet again and guided her to the tunnel exit and fresh air. As they emerged John got his first proper look at Jennifer in days and anger boiled inside him as he realised how battered she was.

Refusing to make her walk any further he picked her up and carefully cradled her as he followed the path he hoped went to the gate.

* * *

**A/N: **Thanks for reading and reviewing. Next chapter should be up tomorrow.


	5. Chapter 5

Sam entered the briefing room and looked onto several despondent faces.

"Anything?" She asked, taking in the tiredness in everyone's eyes.

"Nothing. I'm out of ideas." Rodney confessed. Sam looked at the physicist concerned to see him so defeated. Unlike the others in the room who maintained a professional appearance Rodney's clothes were creased and untucked. His hair stood on end and he gave the appearance of a man who had not slept in days.

"Teyla, Ronon?" Sam questioned.

"None of our contacts know anything." Teyla said, wondering how many others from her life would vanish.

"Lorne?"

"No ma'am, we tried all the addresses McKay pulled out of the gate, but no one remembers seeing them."

The negative news hit Sam hard and she knew the time was coming when she would have to scale back the search. She was trying to come up with a positive course of action when Chuck entered the room.

"Sorry ma'am but we have an unscheduled gate activation. The IDC is one of our friendlies."

"Make sure the marines are in place and lower the shield." Sam ordered, praying it was news of John and Jennifer. As she left the briefing room and looked down to the gate she saw a single female come through.

"Mara?" Rodney whispered. Seeing Sam's blank looks he explained. "A couple of years ago we found a planet with an almost replica city. It's where we got the drones from."

"I remember the report." Sam said.

"Mara was one of the heirs and all over Sheppard, but she did help us." Rodney filled in as he followed the others down the steps.

"Hello Dr McKay, Teyla, Ronon. It is good to see you again." Mara greeted as she looked round the control room.

"Mara." Teyla replied. "This is Colonel Carter, she leads us."

"I know. Colonel Sheppard explained."

"You've seen Sheppard?" McKay asked.

"Yes. He asked me to bring you this." She explained holding out some paper.

"When did you see him?" Sam asked.

"I came straight here from our meeting."

"Was he alone?"

"No, he had a female companion." Mara explained as McKay read the note.

"Were they okay?" Sam pressed Mara as she glanced at McKay.

"No. His companion was barely conscious, but he refused our help. He said he did not want to endanger us." Mara explained as Rodney read aloud.

"Have been held prisoner by rogue Genii. Think I got them all, but escape could be trap. Will wait for you at address below, bring doctor. Keller in bad shape. Hurry."

"Thank you for your help." Sam said. "I don't want to be rude but-"

"I understand, you want your people back." Mara said.

"Thank you. Chuck please dial the gate to send Mara home." Sam ordered before radioing the infirmary.

-00-

"Anything?" Lorne asked as the Jumper came through the gate.

"Give me a minute." Rodney said looking at the scanners. "Yes, I have two lifesigns, five hundred metres from the gate.

"Direction?" Lorne asked impatiently.

"This one. Head to that clearing." Rodney instructed, beginning to feel some hope return.

"Colonel this is Lorne, do you read?" The Major radioed only for Rodney to ask.

"What are you doing?"

"Radioing the Colonel."

"I gathered that, but why. They were taken prisoner, I doubt they'd have been allowed to keep their radios."

"They escaped. They could have got their radios back. And seeing how they were captured Colonel Sheppard may be a bit twitchy and I'd like to warn him that we are here." Lorne argued as he landed the Jumper. As it hit the ground he looked to the back of the Jumper and warned. "Remember this could be a trap." He glanced at his team and ordered. "You guys stay here and guard the Jumper. Everyone else with me."

Stepping out of the Jumper McKay waved his scanner round before saying, pointing to a cave.

"They should be in there." Nodding Ronon pulled his gun before entering calling for Sheppard as he did so.

"Over here Chewie." John's cracked voice called back offering hope and relief to the rescue team.

As the team entered the cavern they saw Jennifer's bruised and battered body resting against John's chest.

"She needs help." The Colonel said as Cole rushed over to the pair.

"What happened?" The doctor asked.

"She was beaten."

As Cole started examining Jennifer, John looked at Rodney and Lorne and warned. "The escape could have been a trap. We could be being tracked or followed."

"I came prepared." Rodney said as he scanned the pair. Finally he said. "They're clear."

"You sure?" Lorne asked, wanting to get them home, but also wanting to keep Atlantis safe.

"I'm sure." Rodney confirmed. "I'm not picking up any tracker or random bits of metal in either of them."

"What happened?" Lorne asked, noticing, as the others were, that John was barely scratched compared to Jennifer.

"Kolya."

"Thought you killed him." Ronon said.

"Not that one. One of his relatives out for revenge." John explained as he cast another guilt-ridden glance at Jennifer. "Stunned us, took us to a planet and beat the crap out of her to get revenge on me."

"Wow, when you piss people off, you really piss them off." Rodney commented earning a stern glance from Teyla who then looked at John and said.

"This is not your fault."

"Tell that to Keller." John said despondently as Lorne asked.

"How did you escape?"

"Part of the hinge on the cell door broke off, it was sharp enough for me to cut the ropes. I thought it was a trap so went through a few gates in case they were following us."

"What happened to Kolya?" Ronon asked.

"He's dead. They're all dead." John said darkly as Cole looked up and announced.

"I'm done. I need her back on Atlantis quickly. Ronon, please carry her, carefully, to the Jumper."

Nodding Ronon swooped down and lifted the still unconscious Jennifer up and carried her out of the cave. The doctor then looked at John and asked.

"How about you?"

"I'm fine." John said clambering to his feet.

"You sure, you have the whole castaway look going for you?" McKay said earning a scowl from John.

"I'm fine." The Colonel reiterated as he made his way to the Jumper, where he sat close to Jennifer, whilst his friends looked on with concern.

* * *

**A/N: **Thanks for reading and reviewing. Next chapter up tomorrow.


	6. Chapter 6

"John, how are you doing?" Sam asked as she joined him at Jennifer's bedside.

"I wasn't the one used as a punch bag." John pointed out, not taking his eyes off the young doctor.

"Don't blame yourself for what happened."

"Kinda hard not to. He was after me and used Jennifer to get his revenge."

"That was not your fault." Sam said before adding. "Jennifer will be okay. Dr Cole said she was lucky."

"I wouldn't call the damaged she sustained lucky." John said irately.

"You and I both know it could have been much worse."

You tell that to Jennifer."

"Can I ask you something?" Sam asked changing tact.

"Sure."

"After you were captured by Kolya, the original one, and tortured because Dr Weir wouldn't give him what he wanted-"

"Hang on that was completely different. I ordered Elizabeth not to give Kolya what he asked for." John interrupted, turning to face Sam. The movement allowing to see how guilt ridden John looked.

"Elizabeth was the one in charge. It was her call. Did you blame her for what you went through?" Sam probed.

"Of course not. She had no choice."

"Because she put the city above you. It was the only thing she could have done. Just like ultimately you had no choice. You couldn't risk the city. Jennifer would have understood that."

"That doesn't make it right. I was meant to protect her. Not sit and watch her get tortured."

"It's easier to sacrifice yourself than watch others do it." Sam agreed as they heard Jennifer start to stir.

John stood and moved closer to Jennifer, as her eyes opened and still revealed fear his heart was consumed by guilt.

"It's okay. We're back home." John told her as she began to take in her surroundings.

"Hey Jennifer." Sam said moving to the CMO's other side, having waved to medical staff.

"..over?" Jennifer croaked.

"Yes it's over. You're safe now." John assured her as a medical team ushered him away from Jennifer.

Sensing the guilt radiating from John, Sam warned him.

"Don't take the blame for this."

"Kinda hard not to." He said before turning and leaving the infirmary.

-00-

"You've been released?" Rodney asked as he saw John storm down the corridor. With out answering, the Colonel went straight past Rodney and disappeared. McKay knew that someone needed to talk to John, but he was pretty sure he wasn't the right person. However, with no other options available he followed John to his quarters.

"What is it McKay?" John snapped as he opened the door.

"Just wanted to check on you." Rodney said.

"I'm great."

"I admit I may not be the most perceptive person here, but even I know that one's a lie."

"You want the truth?" John said coldly. "Fine. Jennifer is lying in the infirmary beaten to a pulp because of me. She was tortured because of me. She, despite being home, is scared because of me."

"It's not your fault that the Kolya family have a genetic predisposition towards insanity." McKay argued, feeling out of his depth. "What happened isn't your fault."

"Really? Whose fault was it then? You know something? She was getting beaten to within an inch of her life and I lied to her." John said, momentarily confusing Rodney until he went on. "I told her to hold on because you were coming. You'd get us out. But you didn't. Were you even looking for us?"

"Of course I was looking." Rodney said after overcoming the shock of hearing the accusation.

"Save it McKay for someone who wants to hear it." John said shutting his door, leaving Rodney standing in the corridor feeling shocked and hurt.

-00-

"Take a seat." Sam instructed as Rodney, Ronon and Teyla entered her office.

"Is there a problem?" Teyla asked, picking up on Sam's sombre mood.

"I think we all know the answer to that one." The Colonel replied causing Ronon to say.

"Sheppard."

"Yes." Carter agreed. "I'm sure I'm not the only one to notice that he has become withdrawn."

"And a jerk." Rodney said, surprising the others in the room.

"It is hardly surprising after what they went through." Teyla pointed out.

"I'm not saying it is." Sam said calmly. "But I am concerned with how hard it has hit him and how he has shut himself away. As far as I know he hasn't left his room since yesterday morning. Seeing Jennifer wake up seemed to have pushed him over the edge."

"He is shouldering all the blame." Teyla agreed. "Currently he won't listen to reason."

"If he continues like this he will be recalled to Earth." Sam said.

"Can't you stop them?" Ronon questioned.

"Unlikely. Even if I could I don't think I would." Sam confessed. "He needs help and seeing we still don't have a replacement for Dr Heightmeyer there isn't anyone qualified to give it to him."

"We can help him." Ronon said.

"Only if he wants to be helped."

"If not you'll turn your back on him?" Ronon questioned, not hiding his disdain.

"Answer me this Ronon. Right now would you be happy going on a mission with John?" Sam asked. She then let the awkward silence linger in the air before saying. "I don't want to send him away, but soon the decision will be out of my hands. If you think you can help him that's great. But we don't have long."

* * *

**A/N: **Thanks for reading and reviewing. Next chapter up in the next couple of days.


	7. Chapter 7

Ronon stood outside John's door waiting for it to open. Knowing that John was in there Ronon relentlessly pressed the chime, trying to force the Colonel to open it. He wasn't sure how long he was there, but eventually his plan worked and the door slid open.

"What?" John snapped, squinting as the harsh light of the corridor penetrated his darkened room.

"We need to talk." Ronon said pushing past John, hitting the light as he did so.

"Geez, can't you take a hint?" John asked covering his eyes as Ronon looked round John's quarters concerned to see the state it was in. John's belongings were tossed round the room and there was a, suspiciously hand sized, dent in a wall. Lying on the floor and on the desk were several empty beer bottles. The Satedan turned to face John, surprised at how bad the Colonel looked.

"What?" John demanded.

"I thought you were better than this." Ronon said bluntly.

"I think the last mission proved I wasn't." John spat back as he searched his room for something to drink.

"I never saw you as a quitter. I thought you stuck by your people."

"Yeah well I'm not up to the task."

"So that's it. You're turning your back on us. Forgetting about Teyla and how desperate she is to find her people. Now the doc. Doesn't the doc deserve better?"

"Yes she does." John said spinning round. "What do you want me to say, I failed her."

"No. You are failing her." Ronon corrected. "She needs to see you and you're hiding."

"When she needed me I turned my back on her."

"No you got her out. Now you've turned your back on her." Ronon said, his voice low and angry.

"How many villages did you destroy when you were being tracked by the Wraith?" John asked. "You really telling me you don't feel responsible for the deaths you caused? Or did your time with the Wraith kill your human side? Apparently I can't ignore mine as easily as you."

Loosing his temper Ronon threw a punch, knocking John to the floor.

"You're pathetic. Keller needs you and you're hiding in here like a coward." The former runner said leaving John's quarters.

As the door shut John lay unmoving on the floor letting the guilt consume him.

-00-

As the alcohol left his system John replayed Ronon's words in his head. He knew Ronon was right, but he felt too much of a coward to see Jennifer. He lay on the floor reliving recent events knowing he could not have done differently yet the feeling of failure was overpowering. He knew he had failed to protect Jennifer and he also knew Ronon was right, Jennifer needed someone and he had turned his back on her. Failing her a second time. Clambering to his feet he stumbled to his mirror and was surprised at how bad he looked. Knowing he couldn't see Jennifer in his condition he showered and shaved and tried to make himself presentable before walking along the corridors of Atlantis towards the infirmary.

As he entered he saw Rodney and Teyla by Jennifer's bedside. Jennifer lay motionless and his two teammates sat quietly so not to disturb her. He was just about to leave when he saw Marie approach Teyla and Rodney. After a brief conversation his teammates stood, Teyla squeezed Jennifer's hand, then they both left leaving Jennifer alone.

John waited in the shadows for Teyla and Rodney to vacate the infirmary and for Marie to run her tests. When she finally disappeared John quietly approached Jennifer's bedside where the doctor lay unmoving. As he did so he immediately picked up on the fact her breathing was wrong and he knew she was feigning sleep.

"They've gone. You don't have to pretend to be asleep." John said. When Jennifer remained motionless John went on. "Okay, you don't want to talk to me either. That one I understand. I wouldn't want to talk to me if I were you either. But I'm hoping you'll listen. I know you're in a dark place right now and it feels like there's no way out, but you have people who care for you who want to help you through this. I can't ever make up for what happened to you, but I'm going to be here for you every step of the way. If you want my help it's there." He then sat in the chair next to her bed, resting his arms on the mattress and said. "As soon as you're ready to talk I'm here." Not knowing what else to say he sat silently and waited.

As time ticked by he watched Jennifer unsure of what else to do. He was aware of various nurses moving round the infirmary, each one with more sense than to try to move him.

It was Jennifer who eventually broke their separation when she stretched her arm over to John and took hold of his hand.

Squeezing her hand he told her "It'll be okay." As silent tears rolled down Jennifer's face.

-00-

"John." Sam said, unable to conceal her surprise when she saw Sheppard at Jennifer's bedside the following morning. "I've been looking for you."

"Well now you've found me." John replied.

"How is she?" Sam asked quietly, letting John's attitude slide.

"The same." John said bluntly as Sam noticed his split lip.

"What happened to your face?"

"Common sense." John said cryptically.

Knowing she wasn't going to get anything more from John Sam said. "I got a message from the SGC this morning. You and Jennifer are being recalled to Earth." When John showed no response to the news Sam continued. "Once you're there you will have to pass psych evals before you can return." Again John remained silent making Sam wonder what was happening inside his head.

* * *

**A/N: **Thanks for reading and reviewing. Next chapter up sometime over the next couple of days.


	8. Chapter 8

"What's up?" Cam asked as he approached Carolyn in the SGC infirmary.

"Nothing." She said without looking up from her notes.

"Sure it is. You've got those two crease marks on your forehead. You only get those when you're worried. So what's up?"

"I'm concerned by my latest patients." The doctor sighed, sitting back.

"Sheppard and Keller? Why?"

"Jennifer is withdrawn and the Colonel only ever displays any signs of normalcy when he is talking to her. The rest of the time he is completely shut down. They keep going like this and neither of them will be going back to Atlantis."

"What does the shrink say?"

"Dr Munroe," Carolyn corrected, "says Jennifer is displaying classic PTSD, but is concerned by Jennifer's complete inability to talk about what happened."

"And Sheppard."

"No idea as the good Colonel keeps skipping the sessions."

"That's not good." Cam commented.

"You think?" Carolyn asked sarcastically.

"Not that surprising though. It must really have eaten him up inside." Cam commented ignoring Carolyn's sarcasm. "He's never struck me as the type of guy who'd like to sit around discussing his issues."

"That seems to be an Air Force trait." Carolyn agreed.

"So what's your plan?"

"Honestly I don't know. The only person Jennifer seems to be comfortable round is Sheppard, but she refuses to talk about what happened even with him."

"Which you know how?"

"I might have overheard a few of their conversations." Carolyn confessed.

"You want me to try?" Cam offered.

"You?" Carolyn asked, not hiding her surprise.

"Thanks for the vote of confidence. But I do have experience in this. Besides you said I was the worse patient you've ever had to put up with. I may be able to help."

"It can't hurt." Carolyn agreed. "As long as you don't teach them any of your bad habits."

-00-

"Hey." Cam greeted from the doorway, as Jennifer looked over he went on. "Carolyn said you were being a difficult patient so I thought I'd come and give you some tips." When Jennifer didn't answer he went on. "You see I'm the king of self pity when I'm stuck in here, probably has something to do with almost dying a few years back but I'm not a shrink so who knows." With still no verbal response from Jennifer he walked over and sat next to her bed, placing the files he was carrying by her bedside. "You need anything for the pain?" This time Jennifer quietly spoke.

"No."

"That's good." Cam replied. "Don't worry, I'm not going to ask you any stupid questions like how are you? That question has to be the stupidest known to man. If you weren't not okay you wouldn't be here so why do people ask? It's not like they want to hear the honest answer either. I'm also not here to talk about what happened. You're old enough and smart enough to have that conversation if you want it. The reason I'm here is because I'm worried about Sheppard."

"Has something happened?" Jennifer asked immediately.

"You tell me. He skips his shrink sessions, he blanks the rest of us. You're the only person he speaks to. You both keep acting like you are and you'll be out of the programme. Perhaps that's what you want, I could understand that. But based on what Sam has said about you I don't think it's true. So if there's any chance that's not what you want you need to act now." Cam said, when Jennifer did not immediately respond he almost gave up but then Jennifer said.

"What happened to me….when people ask…I don't know what I'm meant to say."

"They weren't there. They can't understand." Cam stated. Taking the statement as Cam agreeing with her point Jennifer went on.

"How can they know it'll be okay, when they don't even know what happened?"

"Sheppard was there." Cam pointed out.

"Every time we talk he looks so guilty. I can see it eating him up and it's my fault." Jennifer said. "I can't put him through it again."

"His guilt I get, yours I don't." Cam replied.

"They used me to get to him and I wasn't strong enough. If I-"

"Hold it right there doc, the way I've heard it you did what you needed to do. You held on. That was your job and you did it. You did nothing wrong." Cam assured her. "Sheppard's guilt stems from the fact they hurt you to get to him. If it wasn't for him you would not have been taken or tortured."

"You're wrong. They wanted to get the codes for Atlantis." Jennifer said shaking her head.

"Do you actually know who took you?" Cam asked.

"The Genii."

"Yeah, but do you know which Genii?" Cam pressed.

"Does it make a difference?"

"I'd say so. The guy who took you was called Baccus Kolya. The name mean anything to you?"

"I think I kind of remember hearing it." Jennifer said. "I don't really remember much of what was said in that room though."

"You remember the name from anywhere else?"

"No."

"Okay, history lesson. Acastus Kolya led an elite team of Genii that nearly took control of Atlantis when it was evacuated due to a storm. During the attack Kolya took Dr Weir and Dr McKay hostage and tortured Dr McKay. Sheppard mean while took out most of Kolya's task force. In the end the good guys won, but Kolya escaped. Let's just say after that there was a bit of animosity between the pair. Kolya was banished from the Genii and then captured John and fed him to a Wraith."

"Todd?" Jennifer interrupted.

"That's the one."

"Kolya was behind that?"

"He was. Sheppard escaped, but so did Kolya. Eventually they met again and this time Sheppard finished it. At that stage Sheppard probably thought the fight was over. But it turns out Kolya had a brother who was also banished and followed his brother down the crazy bullbat road."

"How do you know this stuff?"

"I read the mission reports." Cam shrugged. "The point is you were only taken because of the feud between Sheppard and Kolya."

"That doesn't make it his fault."

"You're right. And it sure to hell doesn't make it your fault. But here you both are being consumed by guilt." Cam pointed out. "Anyway, I've talked long enough. I'll let you rest." He said standing. As he did so he reached down and picked up the files he had brought. "I thought you might like these. They're old mission reports. As well as interesting they really help pass the time when you're locked away in an infirmary feeling sorry for yourself." He paused and was about to turn away only to stop and add. "When you're ready to talk there are plenty round here who'll listen. No one is going to give you any answers, but they may help you find them."

-00-

"Colonel Sheppard." Teal'c greeted as he approached the Colonel. In response John silently nodded a greeting. "You are not with Dr Munroe?"

"No. The shrink scene isn't me."

"Yet you can not return to Atlantis with out." Teal'c pointed out.

"No I can't."

"Do you not wish to return?" When John remained silent Teal'c went on. "Perhaps you feel that you are more useful here helping Dr Keller." As John continued to stand in silence Teal'c went on. "Colonel Carter often speaks of you. She said you are a strong leader of high intelligence, but stubborn. The last seems true of many from this planet." He paused and looked at John before going on. "I believe it at the moment is your stubbornness that controls your destiny." He stopped again and waited. After a long drawn out silence the Jaffa once again spoke. "I too have seen my people suffer and been helpless to stop it. I too have turned my back on my friends and betrayed my people. I understand your reluctance to face them again."

"I see Jennifer everyday. I'm there for her as much as I can be." John countered angrily.

"I was not referring to Dr Keller. I was talking about Teyla Emmagan." Noticing John's confused frown he explained. "Did you not promise to help find her people? And yet you are here on Earth, a place almost certainly her people are not."

"Right now Jennifer needs me. What happened to her is my fault and I'll be damned if I don't help her."

"You believe you are helping her?" Teal'c probed.

"Yes. Why do you know something I don't?"

"Indeed."

"Care to elaborate?"

"Dr Keller feels she is responsible for your guilt. She believes she wasn't strong enough and let you down. When she sees you she sees your guilt and is unwilling to add to it by talking about what happened."

"Why hasn't she said something?" John asked.

"To help Dr Keller and Teyla Emmagan you must overcome your guilt." Teal'c said, ignoring John's question.

"And I suppose you have a magic wand to make it all go away?"

"No. But I can teach you kelnorim meditation."

"You think I can meditate my problems away?" John said sceptically.

"It is a path that may help you see your true self and allow you to see where you belong."

"Carter put you up to this?"

"Colonel Carter does not know I am here. But I am here out of respect to her." Teal'c said.

"Glad we cleared that one up."

"If you are prepared to face your demons and discover your true path I will help you." Teal'c said. "I will be waiting in my quarters."

* * *

**A/N: **Thanks for reading and reviewing. Next chapter probably won't be up until Thursday.


	9. Chapter 9

"You're working?" John asked, surprised as he entered Jennifer's room.

"Reading." Jennifer corrected, putting the file down.

"Fun or educational?" John questioned as he walked up to her bed.

"Educational." Jennifer said as John picked up one of the files. As he opened it and saw she was reading his old Kolya based mission reports his face fell and he said.

"I kept meaning to talk to you about this and try to explain things."

"What's to explain? We were in the wrong place at the wrong time."

"Seeing how you've read the mission reports you know there's more to it than that." John pointed out. "The fact you're reading them shows that you need there to be something more to it than that."

"I'm reading them as Cam said I would understand why you're blaming yourself if I read them."

"He did? And do you?"

"No. Kolya was insane and his brother no better. His brother chose an action that would cause you pain. And I was used to get to you." Jennifer said as she shifted on her bed, the movement causing her to wince in pain.

"He would have used whoever I had been with." John said. "He wanted me and was prepared to attack those I cared about. You were hurt because of me. Had I dealt with Kolya at the start none of this would have happened."

"If you'd handed over Atlantis none of this would have happened." Jennifer pointed out. "But that's not a life anyone would have wanted."

John paused as he considered Jennifer's outlook before saying.

"I'm so sorry for what happened to you. If I could make it up to you I would –"

"What happened isn't your fault." Jennifer cut in. "But if you really want to make it up to me you can stop blaming yourself."

In response John half smiled but remained silent, prompting Jennifer to say. "Cam said you weren't attending your therapy sessions."

"Cam says a lot." John responded.

"He also said you're at risk of being thrown off the programme."

"Did he?" John asked, wondering what had possessed the Colonel to burden Jennifer with John's problems.

"Is that what you want?" Jennifer probed.

"Honestly? I wasn't sure. I thought I was better off being here. I actually thought I could help you recover by being here. I was so caught up on what I thought was right I didn't realise I was hindering your recovery until Teal'c pointed it out." Seeing Jennifer was about to speak he quickly continued. "But I've spent the last few hours with Teal'c who has made realise a few things."

"Like?"

"I belong on Atlantis. And right now I'm letting everyone down."

"No you're not."

"Yes I am. You are blaming yourself for my guilt and not talking about what happened to stop me feeling guilty. Rather than helping Teyla find her people I'm here, not doing all I can to return and then there's Ronon and Rodney. I said things to both of them I shouldn't. So back to your original question, no I don't want to be kicked off the programme and knowing that has at least giving me some direction."

"But you still blame yourself?" Jennifer asked.

"Anyway you look at it I was responsible for your safety. I let you down."

"Do you blame me for Dr Weir and Corporals Jones, Miller, Davis and Captain Daniels?" Jennifer asked, listing a handful of those she had lost since becoming CMO.

"Of course not. You did all you could to save them." John said. "But you still blame yourself don't you?" He asked turning it round on Jennifer.

"Hard not to." Jennifer confessed.

"That's the thing with guilt isn't it. From the outside it looks completely unjustifiable, but on the inside there is no escape." John commented. "But as Teal'c drummed into me that doesn't mean you should let your guilt dominate."

"You were sparring?" Jennifer asked.

"Meditating, kind of." John said, causing Jennifer to look confused. "So, how about you?" John asked. "Before you say you're fine remember I've just been honest with you, the least you can do is be honest with me. And don't try to hide things from me."

"After the Bola Kai I couldn't sleep. Every time I shut my eyes I was back there, I could see their faces, smell their breath. It was all so real. I thought it'd be like that this time, but it's not. I don't remember the beatings, maybe I don't want to. I vaguely remember the cell, but what I do remember is the feelings. Pain, fear, feeling lost. I wake up scared, but don't know why. Sometimes it feels like it's too much to handle." She answered, almost whispering at the end. John reached over and silently squeezed her hand. Before he could say anything Jennifer looked up and asked. "How did you cope after Todd?"

"How do you mean?"

"He fed off you, nearly killed you. I know physically you were treated immediately but you must have remembered the feedings."

"I still do." John confessed. "But I used the memories as motivation to train harder so I could avoid being in that situation again. The memories of the pain and the feeling of weakness are still there, they'll never go. But it does get easier." John assured her before a comfortable silence descended. It was John who eventually broke it when he offered. "Here's the deal. I'll start going to my shrink sessions, if you open up in yours."

"I'm not sure I can. It's like there's a wall and I'm afraid what's on the other side. I'm afraid that if I try to remember what happened I won't be strong enough to face it."

"Trust me doc, you're strong enough." John said. For a while another silence descended the room before Jennifer asked.

"Will you come with me….just to a couple."

"I'll come to as many as you want."

-00-

"I'll admit I may have been wrong about you." Carolyn conceded from the corridor as she watched John and Jennifer. "Whatever you said had some affect. In fact what did you say?"

"I just told her Sheppard was in a bad place and mission reports help with self pity." Cameron shrugged.

"You told my patient who has been subjected to torture to pull herself together and help Colonel Sheppard?" Carolyn asked angrily.

"It worked didn't it?" Cam asked as he walked off.

* * *

**A/N: **Thanks for reading and reviewing. Next chapter up tomorrow.


	10. Chapter 10

"Colonel take a seat." Landry ordered two weeks later. Nodding John sat opposite the General and waited.

"I hear Dr Keller is being released from here in the next twenty-four hours." The General started.

"Yes Sir. She's looking forward to seeing her father."

"I'm sure she is. Dr Lam said she's making good progress and you were responsible." Landry went on. The formal reference to his daughter made John wonder if the Landry family was a screwed up as the Sheppard family.

"Seeing I'm responsible for her being in her current state it only seems right I help her get out of it."

"Noble sentiments. How are you doing?" Landry asked.

"Fine Sir, I came out with barely scratch." John said avoiding the question the General wanted answered.

"Tell me something Colonel, do you think you made the right decision?"

"That kind of depends from your point of view. It kept Atlantis safe." John said.

"To the detriment of Dr Keller." Landry pointed out. "Tell me, if you found yourself in a similar situation would you make the same decision?"

"Yes Sir."

"You sure?"

"I'd still feel like crap for doing it. But I'd still make the same decision."

"Just remember Colonel, sometimes you make the right decision, sometimes you make the decision right." Landry said before adding. "Dr Phil."

"Yes Sir." John said politely not sure how to respond. For a moment the John felt an awkward silence in the room before Landry opened a file and said.

"All your assessments are back and you've passed."

"I always was good at tests." John replied.

"And, based on your file, you've always been good at being a smart ass, but that's not a good thing. But regardless we are left with the question do you want to go back? If you feel you need more time I can always lose your file on Walter's desk for two or three weeks."

"I'm ready Sir." John said.

"You sure? You see I grew quite attached to Colonel Carter and I wouldn't want to do something that will cause her any headaches, it sounds like she has quite enough of those already."

"I'm sure." John said. When Landry remained silent John felt compelled to explain. "I admit I may have loss my way for a bit. And I will always feel responsible for what happened, but that doesn't mean I can't make a valuable contribution to Atlantis."

"Fair enough. In that case you can transfer to Midway at 21:00."

"Thank you Sir." John replied. When he didn't move Landry asked.

"Something else on your mind?"

"Actually Sir, I was wondering if you could help me with something?"

-00-

"Mr Keller?" John asked as the door opened.

"Yes. Can I help you?"

"I'm Lieutenant Colonel John Sheppard with the US Air Force." John greeted.

"Jennifer?" The elder Keller asked as he paled.

"I was hoping by not wearing uniform you wouldn't jump to the worse conclusion." John said. "This isn't one of those official visits."

"So she's okay?"

"Can I come in?" John asked, wondering how he was managing to screw the visit up so much.

"Sure." The still pale man responded, desperate to know why John was there. Directing John to a chair he waited nervously for John to begin.

"I serve at the same base as Jennifer. Recently we were taken by hostile forces and she was badly beaten. She's got some cracked ribs and bruising and is currently in an Air Force hospital. She should be released tonight or tomorrow. After which she'll be returned here until she is recovered, assuming she wants to go back." John explained before standing and pacing.

"Why would she be taken? Why was she attacked and not you?" Jennifer's father asked sinking down onto a chair.

"Because I failed her. I'm responsible for her safety and I let her down. She was attacked to make me talk. I can never make up for that." He paused and stopped pacing. "The reason I'm here….This seemed like a good idea at the time." He said more to himself than Jennifer's father. "When we were captive you were the thing that kept her going and she told me the part she hated most about her job is having to lie to you. I can't tell you what we do or even where we're based. But I wanted you to know that what Jennifer does is important and she's damn good at her job. I'm sure you are, but I just wanted to tell you that you should be proud of her." He paused again and then said. "I'm sorry, I probably shouldn't have come. I just thought this might help Jennifer. I should go." John started to turn to the door before pulling out a card and turning back to Jennifer's father. "Regardless of whether she chooses to come back, if you ever need to talk to someone I can be reached on this email. I can't guarantee to respond quickly, lines of communications tend to be slow, but I will get back to you and help in anyway I can. I'm sorry." With that he left, wondering if he had just made things worse.

-00-

"All packed?" John asked Jennifer having returned to the SGC.

"Hey, I thought you'd left." Jennifer said looking round at the Colonel.

"Without saying goodbye?"

"I heard you'd been cleared and were returning to Atlantis and you had left the base."

"I had something to do on Earth before the trip back. I don't leave for Midway for another twenty minutes." John said, not having the courage to confess his visit to Jennifer's father.

"Twenty minutes? Shouldn't you be packing?"

"Not of all us pack for Armageddon." John smiled before sobering and asking. "You going to be okay?"

"I think so." Jennifer said after a pause before saying. "You've never asked."

"Asked what?"

"If I want to go back."

"No I haven't." John confirmed. "I was figuring that if you had decided you'd tell me. I know what I hope you're answer will be, but I'm not going to pressure you one way or the other. Anyway I'd better be going. Good luck and have a good trip back to your dad's."

"Wait." Jennifer said. "I've never thanked you properly. I don't think I could have come through this without you."

"Sure you could." John said. "I just offered a bit of support. You did the hard work."

"Thank you anyway."

"You're welcome." John smiled, just as he was summoned to the gate room. "I really have to go."

"Colonel." Jennifer called after him.

"Yeah."

"Take care of yourself."

"When do I ever not?" John smirked before walking away from Jennifer for, what he worried was, the last time.

* * *

**A/N: **Thanks for reading and reviewing. Penultimate chapter up tomorrow.


	11. Chapter 11

"John. Welcome back." Sam greeted as Sheppard stepped through the Stargate.

"Ma'am." John replied. "Glad to be home."

"How was Earth?"

"Blue, green and planety." John shot back earning a raised eyebrow from Sam who suggested.

"Why don't you get get settled then we'll talk."

"Actually I'd prefer to get that done with now." John pushed.

"Okay, let's go to my office." Sam agreed before heading up the steps.

"How's Jennifer?" Sam questioned as she took a seat.

"Physically she is recovering well. Dr Lam took good care of her."

"And emotionally?"

"Time will tell. But your old team are keeping an eye on her."

"How about you?"

"I'm fine. Wouldn't have been allowed back if I wasn't." John replied.

"And off the record?" Sam probed.

"As much as I hate to admit it, the counselling helped."

"Really? I heard you skipped your sessions." Sam said.

"I meant the unofficial Teal'c ones." John clarified, although he assumed Sam already knew that.

"That's good." Sam smiled although deep down she still had lingering doubts over John's truthfulness. "So do you think you're ready to return to duty?"

"I do." John said. "But if you have any doubts I'm sure Ronon would be only too happy to watch me and stun me at the first sign of trouble."

"He seems to enjoy that." Sam agreed. "You sure you're ready?"

"I'm sure."

"Okay then, I'll add you to tomorrow's mission. The briefing is in three hours."

"Thank you. So what's been happening here?"

"It's all been quiet, by Atlantis standards anyway. Although, Rodney did trigger a city wide alert when he tried to recalibrate the sensors."

"Fun."

"That's one way of looking at it." Sam said. "Go see you team I know they've missed you."

"Will do." John said standing and walking to the door.

"John." Sam called.

"Yeah?"

"It's good to have you back."

"Good to be back." He replied honestly and was about to open the door when he suddenly remembered what he was carrying. "I nearly forgot." He commented as he rummaged in his bag. Finally he pulled out a small package and tossed it to Sam.

"General O'Neill sends his regards and coffee."

-00-

"Guys." John said as he walked over to their table.

"John!" Teyla smiled. "Welcome home."

"Thank you." John replied. "Mind if I sit?"

"Of course not." Teyla said before asking. "How was Earth?"

"Dull." John replied as he sat down. "I spent most of my time at the SGC so didn't actually see much of it."

"And Jennifer?"

"Recovering. She's spending some time with her dad."

"I'm sure that will help." Teyla said.

"I hope so." John said.

"Does this mean you're not crazy anymore?" Rodney asked less than tactfully.

"I was never crazy." John said. Knowing Rodney was about to comment further he continued. "So anyway I wanted to apologise for how I acted. I was-"

"A jerk?" Rodney suggested.

"Not what I was going to say, but okay. I said some things I shouldn't have and took my anger out on you. I shouldn't have done that either. I'm sorry." John said looking sat his team.

"We understand." Teyla said, although the two men looked less forgiving.

"I know you've probably lost a bit of faith in me, but I promise I will make it up to you." John stated looking directly at Ronon who remained unmoved.

"You sure you're okay?" Rodney asked.

"I'm sure. You can even see my certificate if you want."

"Too easy to get one of those. If you're really you as in the old you answer me this, who is the best Captain?" Rodney asked.

"Seriously? You are basing my sanity on who I believe is the best Captain?" John asked.

"Yes. Each Captain had a unique personality and outlook on life. Who you chose is a reflection of what you are feeling." McKay argued.

"Fine. Kirk." John said. "Do I pass?"

For a moment Rodney said nothing before finally conceding. "Yes. But for the record Picard was the best Captain, although I concede TOS was better then TNG."

"Any idea?" Ronon asked Teyla, who shook her head, looking as baffled as Ronon felt.

"How can you not have picked up who Kirk is by now?" Rodney asked with disdain.

"I know of him." Teyla said. "He is the Captain who loses his shirt. But I do not understand TOS or TNG."

"Seriously? You've been in the city for years." Rodney commented before turning his focus back to John and asking. "So you bring us anything back?"

"Like what?"

"Like something that would help support your apology."

"You want me to buy your forgiveness? I thought I'd just passed your test."

"You did, well one of them anyway. There are plenty more."

"This is sounding like blackmail." John pointed out.

"So that's a no?" Rodney asked sounding disappointed.

"I didn't say that." John pointed out.

"So what is it and football recordings don't count."

"Hershey's and a movie."

"Which one?"

"Alien." John said, finally getting a reaction from Ronon, who displayed a glimmer of excitement.

"Perhaps it would be best if Rodney did not eat the chocolate before or during the movie." Teyla suggest, recalling Rodney's previous experience.

"Funny." Rodney said standing. "Well if you'll excuse me I have the city to run."

"You replace Carter in my absence?" John asked as Rodney walked off.

"I have some things to attend to as well." Teyla said, knowing that John needed to speak to Ronon alone.

John waited until Teyla had disappeared before saying. "Look, I'm sorry. What I said, it wasn't me, well it was obviously, but that's not how I felt, well feel. I was messed up and you took the brunt of it. I'm sorry. I guess I should thank you as well. I mean you did knock some common sense into me." Having said all he could think of he waited for a response from Ronon. When the former runner shrugged John asked. "So we're good?"

"Yeah." Ronon eventually replied before standing and saying. "Let's go."

"Where? The briefing is still over an hour away."

"Sparring." Ronon said. "You need more common sense."

* * *

**A/N: **Thanks for reading and reviewing. Final chapter up tomorrow.


	12. Chapter 12

"Hey." John smiled as Jennifer's door slid open.

"Hi." The doctor replied warmly.

"Carter said you were back."

"You're surprised."

"A little. After what happened I assumed you'd want to stay away."

"It crossed my mind." Jennifer confessed.

"So why are you here?"

"I've never really fitted anywhere. But here, it was starting to feel like I belonged. When we were in that cell you had so much faith in your team, that they'd come and get us. That trust is special and unique and I don't want to leave the chance of having something like that because of a bad experience."

"Well I'm glad you're back."

"Thanks." Jennifer said before an awkward silence descended. It was Jennifer who broke it by saying. "So my dad told me you came to visit him."

"Yeah about that. It was a stupid idea and I'm sorry if I made things worse." John said sheepishly.

"Worse? Why would you think that?"

"Well I didn't really think it through and I thought it was a good idea right up until I started speaking. I shouldn't have gone."

"You didn't make anything worse." Jennifer said. "I think it helped my dad worry less about the fact I chose to come back."

"Really? Because I thought he seemed a lot more worried after I spoke to him."

"Confused maybe." Jennifer conceded. "But he liked you."

"He did?"

"He did." Jennifer confirmed before asking. "So how are you doing?"

"Getting there. Ronon's keeping me on the straight and narrow."

"Does that mean you're overworking my infirmary?"

"I view it as contributing to their training." John smiled before asking. "How about you? You handling everything okay?"

"Better than I was. After you left I had a couple of weeks on intensive therapy sessions, which helped."

"I thought you were going back to Chippewa Falls?"

"I did. The Apollo was in orbit getting repaired so I beamed up there everyday to meet Dr Munroe. I was cleared to return last week after that I spent some time soul searching and chose to come back a couple of days ago. I'm not saying I don't have bad days, but the good ones are more frequent."

"That's good. Just remember the offer is still there. I'm here any time you need to talk." John offered.

"Thank you." Jennifer said sincerely, although John wasn't convinced she would take him up on the offer. The two stood in silence for a moment before John asked.

"So how are the ribs?"

"Getting there slowly. Still a while off going through the gate again. Which, is probably a good thing."

"You can't avoid it forever." John pointed out.

"I know, but I'll take two weeks."

"Fair enough. So can you walk around now?"

"As long as I go slow."

"Good. In that case are you coming?"

"Coming where?"

"Movie night. The whole team is going to be there." John said, sensing her reluctance he went on. "There's chocolate and popcorn and we won't keep you out too late."

"I don't want to intrude."

"You won't be. Besides you're part of the team. I'm not leaving without you." John said.

"Colonel, I –"

"Doc," John said. "Seeing how we are off duty and all and seeing how much we've been through together recently, you think you can use my name rather than my rank?"

"Fine, Sheppard I-"

"I meant John, but baby steps." The Colonel interrupted again.

"John," Jennifer said, "I appreciate the offer b-"

"Excellent. Let's go." John smiled.

"You're not giving up are you?" Jennifer asked.

"No."

"Fine, I'll come." Jennifer conceded, giving up arguing.

"That's my girl." John replied stepping away from the door so Jennifer could step out of her quarters.

As they walked slowly down the corridor Jennifer said.

"Co- John, I know I said this on Earth, but thank you for sticking by me and being there for me, it meant a lot to me. If it weren't for you I wouldn't be here."

Stopping John placed his hands on Jennifer and gently turned her to face him. "There's no need to thank me. And you are strong enough to come through every challenge you face, with or without help. And if anyone here should be doing the thanking it's me. Despite what you'd been through you were more concerned with helping me and getting me back on the right track." John stared down at the doctor, beginning to feel a real connection. He was about to say something when the door behind Jennifer opened.

"You're here. At last. What took you so long?" Rodney exclaimed. "My blood sugar levels are dropping dangerously low."

"Good thing we have a doctor then." John said glaring at Rodney. "Not to mention all the chocolate in the room."

"Ronon said I couldn't start it until you were back. But here you are so let's get it started." Rodney said moving back inside John's quarters. Noticing John and Jennifer not moving he asked. "Aren't you coming?"

"Yes Rodney, we're coming." John said, taking his hands off Jennifer.

"Welcome back by the way." Rodney said to Jennifer as he moved further into the room.

"Shall we?" John asked gesturing to the room. As Jennifer started to turn he added. "I really am glad you came back." With that the pair walked into John's quarters.

_**-The End**_

* * *

_****_**A/N: **Thank you for reading and reviewing. I hope you enjoyed it.


End file.
